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November 2013, Volume 9, Issue 11
- 1-9 Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity
by Kejian Wang & Jiazhi Sun & Shufeng Zhou & Chunling Wan & Shengying Qin & Can Li & Lin He & Lun Yang - 1-9 Beyond GLMs: A Generative Mixture Modeling Approach to Neural System Identification
by Lucas Theis & Andrè Maia Chagas & Daniel Arnstein & Cornelius Schwarz & Matthias Bethge - 1-10 MicroRNA-Gene Association As a Prognostic Biomarker in Cancer Exposes Disease Mechanisms
by Rotem Ben-Hamo & Sol Efroni - 1-10 Distribution of the Fittest Individuals and the Rate of Muller's Ratchet in a Model with Overlapping Generations
by Jakob J Metzger & Stephan Eule - 1-11 Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data
by Weronika Sikora-Wohlfeld & Marit Ackermann & Eleni G Christodoulou & Kalaimathy Singaravelu & Andreas Beyer - 1-12 Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins
by Debabani Ganguly & Weihong Zhang & Jianhan Chen - 1-13 Mapping the Structural and Dynamical Features of Kinesin Motor Domains
by Guido Scarabelli & Barry J Grant - 1-13 A Data-Driven Mathematical Model of CA-MRSA Transmission among Age Groups: Evaluating the Effect of Control Interventions
by Xiaoxia Wang & Sarada Panchanathan & Gerardo Chowell - 1-14 A Neurocomputational Model of the Mismatch Negativity
by Falk Lieder & Klaas E Stephan & Jean Daunizeau & Marta I Garrido & Karl J Friston - 1-14 Improving the Modeling of Disease Data from the Government Surveillance System: A Case Study on Malaria in the Brazilian Amazon
by Denis Valle & James Clark - 1-14 Average Is Optimal: An Inverted-U Relationship between Trial-to-Trial Brain Activity and Behavioral Performance
by Biyu J He & John M Zempel - 1-14 A Computational Model of Liver Iron Metabolism
by Simon Mitchell & Pedro Mendes - 1-15 Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos
by Julian E Fuchs & Susanne von Grafenstein & Roland G Huber & Christian Kramer & Klaus R Liedl - 1-15 Optimality Conditions for Cell-Fate Heterogeneity That Maximize the Effects of Growth Factors in PC12 Cells
by Kazunari Mouri & Yasushi Sako - 1-16 Receptor Concentration and Diffusivity Control Multivalent Binding of Sv40 to Membrane Bilayers
by Oliwia M Szklarczyk & Nélido González-Segredo & Philipp Kukura & Ariella Oppenheim & Daniel Choquet & Vahid Sandoghdar & Ari Helenius & Ivo F Sbalzarini & Helge Ewers - 1-16 Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks
by Takeshi Hase & Samik Ghosh & Ryota Yamanaka & Hiroaki Kitano - 1-16 Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data
by Ridvan Eksi & Hong-Dong Li & Rajasree Menon & Yuchen Wen & Gilbert S Omenn & Matthias Kretzler & Yuanfang Guan - 1-16 Predictive Coding of Dynamical Variables in Balanced Spiking Networks
by Martin Boerlin & Christian K Machens & Sophie Denève - 1-17 Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations
by Noa Chapal-Ilani & Yosef E Maruvka & Adam Spiro & Yitzhak Reizel & Rivka Adar & Liran I Shlush & Ehud Shapiro - 1-18 Dread and the Disvalue of Future Pain
by Giles W Story & Ivaylo Vlaev & Ben Seymour & Joel S Winston & Ara Darzi & Raymond J Dolan - 1-28 Stochastic Computations in Cortical Microcircuit Models
by Stefan Habenschuss & Zeno Jonke & Wolfgang Maass
October 2013, Volume 9, Issue 10
- 1-1 How Can PLOS Computational Biology Help the Biological Sciences?
by Ruth Nussinov - 1-3 Explain Bioinformatics to Your Grandmother!
by Virginie Bernard & Magali Michaut - 1-3 APBioNet—Transforming Bioinformatics in the Asia-Pacific Region
by Asif M Khan & Tin Wee Tan & Christian Schönbach & Shoba Ranganathan - 1-4 Ten Simple Rules for Reproducible Computational Research
by Geir Kjetil Sandve & Anton Nekrutenko & James Taylor & Eivind Hovig - 1-9 Molecular Mechanical Differences between Isoforms of Contractile Actin in the Presence of Isoforms of Smooth Muscle Tropomyosin
by Lennart Hilbert & Genevieve Bates & Horia N Roman & Jenna L Blumenthal & Nedjma B Zitouni & Apolinary Sobieszek & Michael C Mackey & Anne-Marie Lauzon - 1-10 ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data
by André Yoshiaki Kashiwabara & Ígor Bonadio & Vitor Onuchic & Felipe Amado & Rafael Mathias & Alan Mitchell Durham - 1-10 Feature Selection Methods for Identifying Genetic Determinants of Host Species in RNA Viruses
by Ricardo Aguas & Neil M Ferguson - 1-10 Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening
by Arnab Bhattacherjee & Stefan Wallin - 1-11 Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes
by Ryan Suderman & Eric J Deeds - 1-11 Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins
by Fan Jin & Chen Yu & Luhua Lai & Zhirong Liu - 1-11 A Complex-Valued Firing-Rate Model That Approximates the Dynamics of Spiking Networks
by Evan S Schaffer & Srdjan Ostojic & L F Abbott - 1-12 The Molecular Mechanism of Ion-Dependent Gating in Secondary Transporters
by Chunfeng Zhao & Sergei Yu Noskov - 1-12 The Lazy Visual Word Form Area: Computational Insights into Location-Sensitivity
by Thomas Hannagan & Jonathan Grainger - 1-13 dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data
by Dongjun Chung & Dan Park & Kevin Myers & Jeffrey Grass & Patricia Kiley & Robert Landick & Sündüz Keleş - 1-13 Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data
by Joshua G Schraiber & Yulia Mostovoy & Tiffany Y Hsu & Rachel B Brem - 1-14 Cellular Adaptation Facilitates Sparse and Reliable Coding in Sensory Pathways
by Farzad Farkhooi & Anja Froese & Eilif Muller & Randolf Menzel & Martin P Nawrot - 1-14 Analysis of Initial Cell Spreading Using Mechanistic Contact Formulations for a Deformable Cell Model
by Tim Odenthal & Bart Smeets & Paul Van Liedekerke & Engelbert Tijskens & Hans Van Oosterwyck & Herman Ramon - 1-14 Comprehensive Repertoire of Foldable Regions within Whole Genomes
by Guilhem Faure & Isabelle Callebaut - 1-15 GINI: From ISH Images to Gene Interaction Networks
by Kriti Puniyani & Eric P Xing - 1-15 Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision
by Luca Grieco & Laurence Calzone & Isabelle Bernard-Pierrot & François Radvanyi & Brigitte Kahn-Perlès & Denis Thieffry - 1-15 Attention-Dependent Modulation of Cortical Taste Circuits Revealed by Granger Causality with Signal-Dependent Noise
by Qiang Luo & Tian Ge & Fabian Grabenhorst & Jianfeng Feng & Edmund T Rolls - 1-15 Deciding Not to Decide: Computational and Neural Evidence for Hidden Behavior in Sequential Choice
by Sebastian Gluth & Jörg Rieskamp & Christian Büchel - 1-15 Dynamic Rendering of the Heterogeneous Cell Response to Anticancer Treatments
by Francesca Falcetta & Monica Lupi & Valentina Colombo & Paolo Ubezio - 1-16 The Influence of Synaptic Weight Distribution on Neuronal Population Dynamics
by Ramakrishnan Iyer & Vilas Menon & Michael Buice & Christof Koch & Stefan Mihalas - 1-16 The Convallis Rule for Unsupervised Learning in Cortical Networks
by Pierre Yger & Kenneth D Harris - 1-16 Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster
by Kolja Becker & Eva Balsa-Canto & Damjan Cicin-Sain & Astrid Hoermann & Hilde Janssens & Julio R Banga & Johannes Jaeger - 1-17 A Brain-Machine Interface for Control of Medically-Induced Coma
by Maryam M Shanechi & Jessica J Chemali & Max Liberman & Ken Solt & Emery N Brown - 1-18 Novel Methods for Analysing Bacterial Tracks Reveal Persistence in Rhodobacter sphaeroides
by Gabriel Rosser & Alexander G Fletcher & David A Wilkinson & Jennifer A de Beyer & Christian A Yates & Judith P Armitage & Philip K Maini & Ruth E Baker - 1-18 An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis
by Pralay Mitra & David Shultis & Jeffrey R Brender & Jeff Czajka & David Marsh & Felicia Gray & Tomasz Cierpicki & Yang Zhang
September 2013, Volume 9, Issue 9
- 1-2 ISCB Computational Biology Wikipedia Competition
by Alex Bateman & Janet Kelso & Daniel Mietchen & Geoff Macintyre & Tomás Di Domenico & Thomas Abeel & Darren W Logan & Predrag Radivojac & Burkhard Rost - 1-4 The Regional Student Group Program of the ISCB Student Council: Stories from the Road
by Geoff Macintyre & Magali Michaut & Thomas Abeel - 1-4 Ten Simple Rules for Cultivating Open Science and Collaborative R&D
by Hassan Masum & Aarthi Rao & Benjamin M Good & Matthew H Todd & Aled M Edwards & Leslie Chan & Barry A Bunin & Andrew I Su & Zakir Thomas & Philip E Bourne - 1-5 Using Biological Pathway Data with Paxtools
by Emek Demir & Özgün Babur & Igor Rodchenkov & Bülent Arman Aksoy & Ken I Fukuda & Benjamin Gross & Onur Selçuk Sümer & Gary D Bader & Chris Sander - 1-8 Collective Dynamics Underlying Allosteric Transitions in Hemoglobin
by Martin D Vesper & Bert L de Groot - 1-9 Predictive Modeling of In Vivo Response to Gemcitabine in Pancreatic Cancer
by James J Lee & Justin Huang & Christopher G England & Lacey R McNally & Hermann B Frieboes - 1-10 From Cellular Characteristics to Disease Diagnosis: Uncovering Phenotypes with Supercells
by Julián Candia & Ryan Maunu & Meghan Driscoll & Angélique Biancotto & Pradeep Dagur & J Philip McCoy Jr & H Nida Sen & Lai Wei & Amos Maritan & Kan Cao & Robert B Nussenblatt & Jayanth R Banavar & Wolfgang Losert - 1-12 Genome-Wide Signatures of Transcription Factor Activity: Connecting Transcription Factors, Disease, and Small Molecules
by Jing Chen & Zhen Hu & Mukta Phatak & John Reichard & Johannes M Freudenberg & Siva Sivaganesan & Mario Medvedovic - 1-12 Polycation-π Interactions Are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family
by Jianhui Song & Sheung Chun Ng & Peter Tompa & Kevin A W Lee & Hue Sun Chan - 1-12 Spike Triggered Covariance in Strongly Correlated Gaussian Stimuli
by Johnatan Aljadeff & Ronen Segev & Michael J Berry II & Tatyana O Sharpee - 1-12 Potential Role of a Bistable Histidine Kinase Switch in the Asymmetric Division Cycle of Caulobacter crescentus
by Kartik Subramanian & Mark R Paul & John J Tyson - 1-12 Predicting Odor Perceptual Similarity from Odor Structure
by Kobi Snitz & Adi Yablonka & Tali Weiss & Idan Frumin & Rehan M Khan & Noam Sobel - 1-12 Antimicrobial Peptides Design by Evolutionary Multiobjective Optimization
by Giuseppe Maccari & Mariagrazia Di Luca & Riccardo Nifosí & Francesco Cardarelli & Giovanni Signore & Claudia Boccardi & Angelo Bifone - 1-13 Adaptation Dynamics in Densely Clustered Chemoreceptors
by William Pontius & Michael W Sneddon & Thierry Emonet - 1-14 Motility Enhancement through Surface Modification Is Sufficient for Cyanobacterial Community Organization during Phototaxis
by Tristan Ursell & Rosanna Man Wah Chau & Susanne Wisen & Devaki Bhaya & Kerwyn Casey Huang - 1-15 Frequency Response of a Protein to Local Conformational Perturbations
by Dilek Eren & Burak Alakent - 1-16 From Birdsong to Human Speech Recognition: Bayesian Inference on a Hierarchy of Nonlinear Dynamical Systems
by Izzet B Yildiz & Katharina von Kriegstein & Stefan J Kiebel - 1-16 Task-Based Core-Periphery Organization of Human Brain Dynamics
by Danielle S Bassett & Nicholas F Wymbs & M Puck Rombach & Mason A Porter & Peter J Mucha & Scott T Grafton - 1-16 Mechanistic Model of Natural Killer Cell Proliferative Response to IL-15 Receptor Stimulation
by Yun M Zhao & Anthony R French - 1-16 Target Inhibition Networks: Predicting Selective Combinations of Druggable Targets to Block Cancer Survival Pathways
by Jing Tang & Leena Karhinen & Tao Xu & Agnieszka Szwajda & Bhagwan Yadav & Krister Wennerberg & Tero Aittokallio - 1-16 Semi-automated Curation of Metabolic Models via Flux Balance Analysis: A Case Study with Mycoplasma gallisepticum
by Eddy J Bautista & Joseph Zinski & Steven M Szczepanek & Erik L Johnson & Edan R Tulman & Wei-Mei Ching & Steven J Geary & Ranjan Srivastava - 1-18 The Next Generation of Transcription Factor Binding Site Prediction
by Anthony Mathelier & Wyeth W Wasserman - 1-19 Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs
by Ioannis N Melas & Regina Samaga & Leonidas G Alexopoulos & Steffen Klamt - 1-20 Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors
by Linhui Hao & Qiuling He & Zhishi Wang & Mark Craven & Michael A Newton & Paul Ahlquist - 1-27 Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization
by Rudi Agius & Mieczyslaw Torchala & Iain H Moal & Juan Fernández-Recio & Paul A Bates
August 2013, Volume 9, Issue 8
- 1-3 International Society for Computational Biology Welcomes Its Newest Class of Fellows
by Christiana N Fogg & Diane E Kovats - 1-10 Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms
by Ohad Manor & Eran Segal - 1-10 Software for Computing and Annotating Genomic Ranges
by Michael Lawrence & Wolfgang Huber & Hervé Pagès & Patrick Aboyoun & Marc Carlson & Robert Gentleman & Martin T Morgan & Vincent J Carey - 1-11 Sensory Information and Encounter Rates of Interacting Species
by Andrew M Hein & Scott A McKinley - 1-11 Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization
by Guillermo Rodrigo & Thomas E Landrain & Eszter Majer & José-Antonio Daròs & Alfonso Jaramillo - 1-12 A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays
by Neta S Zuckerman & Yair Noam & Andrea J Goldsmith & Peter P Lee - 1-14 Determinants of Beat-to-Beat Variability of Repolarization Duration in the Canine Ventricular Myocyte: A Computational Analysis
by Jordi Heijman & Antonio Zaza & Daniel M Johnson & Yoram Rudy & Ralf L M Peeters & Paul G A Volders & Ronald L Westra - 1-14 Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths
by Chunhe Li & Jin Wang - 1-14 Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases
by Simona Mariani & Daniele Dell'Orco & Angelo Felline & Francesco Raimondi & Francesca Fanelli - 1-14 Priors Engaged in Long-Latency Responses to Mechanical Perturbations Suggest a Rapid Update in State Estimation
by Frédéric Crevecoeur & Stephen H Scott - 1-15 Model-Based Analysis of HER Activation in Cells Co-Expressing EGFR, HER2 and HER3
by Harish Shankaran & Yi Zhang & Yunbing Tan & Haluk Resat - 1-15 Visual Nonclassical Receptive Field Effects Emerge from Sparse Coding in a Dynamical System
by Mengchen Zhu & Christopher J Rozell - 1-15 Parameter Trajectory Analysis to Identify Treatment Effects of Pharmacological Interventions
by Christian A Tiemann & Joep Vanlier & Maaike H Oosterveer & Albert K Groen & Peter A J Hilbers & Natal A W van Riel - 1-16 Characteristic Effects of Stochastic Oscillatory Forcing on Neural Firing: Analytical Theory and Comparison to Paddlefish Electroreceptor Data
by Christoph Bauermeister & Tilo Schwalger & David F Russell & Alexander B Neiman & Benjamin Lindner - 1-17 From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction
by Simona Cocco & Remi Monasson & Martin Weigt - 1-20 Shape Similarity, Better than Semantic Membership, Accounts for the Structure of Visual Object Representations in a Population of Monkey Inferotemporal Neurons
by Carlo Baldassi & Alireza Alemi-Neissi & Marino Pagan & James J DiCarlo & Riccardo Zecchina & Davide Zoccolan - 1-23 Top-Down Beta Rhythms Support Selective Attention via Interlaminar Interaction: A Model
by Jung H Lee & Miles A Whittington & Nancy J Kopell
July 2013, Volume 9, Issue 7
- 1-4 Ten Simple Rules for Writing a Literature Review
by Marco Pautasso - 1-10 Co-expression Profiling of Autism Genes in the Mouse Brain
by Idan Menashe & Pascal Grange & Eric C Larsen & Sharmila Banerjee-Basu & Partha P Mitra - 1-10 Insertion of the Ca2+-Independent Phospholipase A2 into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations
by Denis Bucher & Yuan-Hao Hsu & Varnavas D Mouchlis & Edward A Dennis & J Andrew McCammon - 1-10 The Minimal Complexity of Adapting Agents Increases with Fitness
by Nikhil J Joshi & Giulio Tononi & Christof Koch - 1-11 Consistent Estimation of Gibbs Energy Using Component Contributions
by Elad Noor & Hulda S Haraldsdóttir & Ron Milo & Ronan M T Fleming - 1-12 Spatial Stochastic Dynamics Enable Robust Cell Polarization
by Michael J Lawson & Brian Drawert & Mustafa Khammash & Linda Petzold & Tau-Mu Yi - 1-13 Gain Control Network Conditions in Early Sensory Coding
by Eduardo Serrano & Thomas Nowotny & Rafael Levi & Brian H Smith & Ramón Huerta - 1-13 Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein
by Burcu Aykaç Fas & Yusuf Tutar & Türkan Haliloğlu - 1-14 Statistical Analysis of Molecular Signal Recording
by Joshua I Glaser & Bradley M Zamft & Adam H Marblestone & Jeffrey R Moffitt & Keith Tyo & Edward S Boyden & George Church & Konrad P Kording - 1-14 Hierarchical Modeling for Rare Event Detection and Cell Subset Alignment across Flow Cytometry Samples
by Andrew Cron & Cécile Gouttefangeas & Jacob Frelinger & Lin Lin & Satwinder K Singh & Cedrik M Britten & Marij J P Welters & Sjoerd H van der Burg & Mike West & Cliburn Chan - 1-17 Interaction of Motility, Directional Sensing, and Polarity Modules Recreates the Behaviors of Chemotaxing Cells
by Changji Shi & Chuan-Hsiang Huang & Peter N Devreotes & Pablo A Iglesias - 1-17 A Family of Algorithms for Computing Consensus about Node State from Network Data
by Eleanor R Brush & David C Krakauer & Jessica C Flack - 1-18 A Mixture of Delta-Rules Approximation to Bayesian Inference in Change-Point Problems
by Robert C Wilson & Matthew R Nassar & Joshua I Gold - 1-18 Inferring Nonlinear Neuronal Computation Based on Physiologically Plausible Inputs
by James M McFarland & Yuwei Cui & Daniel A Butts - 1-23 Frequency Dependence of Signal Power and Spatial Reach of the Local Field Potential
by Szymon Łęski & Henrik Lindén & Tom Tetzlaff & Klas H Pettersen & Gaute T Einevoll
June 2013, Volume 9, Issue 6
- 1-9 Scrutinizing MHC-I Binding Peptides and Their Limits of Variation
by Christian P Koch & Anna M Perna & Max Pillong & Nickolay K Todoroff & Paul Wrede & Gerd Folkers & Jan A Hiss & Gisbert Schneider - 1-11 Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression
by Nanye Long & Samuel P Dickson & Jessica M Maia & Hee Shin Kim & Qianqian Zhu & Andrew S Allen - 1-11 The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum
by William R Harcombe & Nigel F Delaney & Nicholas Leiby & Niels Klitgord & Christopher J Marx - 1-13 Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer
by Kristian Ovaska & Filomena Matarese & Korbinian Grote & Iryna Charapitsa & Alejandra Cervera & Chengyu Liu & George Reid & Martin Seifert & Hendrik G Stunnenberg & Sampsa Hautaniemi - 1-14 Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach
by Meagan C Small & Pedro Lopes & Rodrigo B Andrade & Alexander D MacKerell Jr - 1-15 Patterns of Proliferative Activity in the Colonic Crypt Determine Crypt Stability and Rates of Somatic Evolution
by Rui Zhao & Franziska Michor - 1-16 Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study
by Jörg Bornschein & Marc Henniges & Jörg Lücke - 1-17 Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1
by Lyudmyla Dorosh & Olesya A Kharenko & Nandhakishore Rajagopalan & Michele C Loewen & Maria Stepanova - 1-19 Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins
by Louis-François Handfield & Yolanda T Chong & Jibril Simmons & Brenda J Andrews & Alan M Moses - 1-19 PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data
by Gabriel E Hoffman & Benjamin A Logsdon & Jason G Mezey - 1-20 Dynamic Excitatory and Inhibitory Gain Modulation Can Produce Flexible, Robust and Optimal Decision-making
by Ritwik K Niyogi & KongFatt Wong-Lin
May 2013, Volume 9, Issue 5
- 1-1 A Kinetic Platform to Determine the Fate of Nitric Oxide in Escherichia coli
by Jonathan L Robinson & Mark P Brynildsen - 1-9 Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA
by Tobias Linder & Bert L de Groot & Anna Stary-Weinzinger - 1-9 The Emergence of Environmental Homeostasis in Complex Ecosystems
by James G Dyke & Iain S Weaver - 1-10 Host Resistance, Population Structure and the Long-Term Persistence of Bubonic Plague: Contributions of a Modelling Approach in the Malagasy Focus
by Fanny Gascuel & Marc Choisy & Jean-Marc Duplantier & Florence Débarre & Carine Brouat - 1-11 Polymorphisms in the F8 Gene and MHC-II Variants as Risk Factors for the Development of Inhibitory Anti-Factor VIII Antibodies during the Treatment of Hemophilia A: A Computational Assessment
by Gouri Shankar Pandey & Chen Yanover & Tom E Howard & Zuben E Sauna - 1-11 Hybrid Equation/Agent-Based Model of Ischemia-Induced Hyperemia and Pressure Ulcer Formation Predicts Greater Propensity to Ulcerate in Subjects with Spinal Cord Injury
by Alexey Solovyev & Qi Mi & Yi-Ting Tzen & David Brienza & Yoram Vodovotz - 1-11 Testing Whether Humans Have an Accurate Model of Their Own Motor Uncertainty in a Speeded Reaching Task
by Hang Zhang & Nathaniel D Daw & Laurence T Maloney - 1-12 Long-range Order in Canary Song
by Jeffrey E Markowitz & Elizabeth Ivie & Laura Kligler & Timothy J Gardner - 1-12 Effect of Regulatory Architecture on Broad versus Narrow Sense Heritability
by Yunpeng Wang & Jon Olav Vik & Stig W Omholt & Arne B Gjuvsland - 1-13 Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations
by Xiaodong Cai & Juan Andrés Bazerque & Georgios B Giannakis - 1-13 Critical Role of Transient Activity of MT1-MMP for ECM Degradation in Invadopodia
by Ayako Watanabe & Daisuke Hosino & Naohiko Koshikawa & Motoharu Seiki & Takashi Suzuki & Kazuhisa Ichikawa - 1-13 The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch
by Wei Huang & Joohyun Kim & Shantenu Jha & Fareed Aboul-ela - 1-13 Modeling and Measuring Signal Relay in Noisy Directed Migration of Cell Groups
by Can Guven & Erin Rericha & Edward Ott & Wolfgang Losert - 1-14 Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation
by Haipeng Li & Thomas Wiehe - 1-14 STL-based Analysis of TRAIL-induced Apoptosis Challenges the Notion of Type I/Type II Cell Line Classification
by Szymon Stoma & Alexandre Donzé & François Bertaux & Oded Maler & Gregory Batt - 1-16 Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling
by Erhan Bilal & Janusz Dutkowski & Justin Guinney & In Sock Jang & Benjamin A Logsdon & Gaurav Pandey & Benjamin A Sauerwine & Yishai Shimoni & Hans Kristian Moen Vollan & Brigham H Mecham & Oscar M Rueda & Jorg Tost & Christina Curtis & Mariano J Alvarez & Vessela N Kristensen & Samuel Aparicio & Anne-Lise Børresen-Dale & Carlos Caldas & Andrea Califano & Stephen H Friend & Trey Ideker & Eric E Schadt & Gustavo A Stolovitzky & Adam A Margolin - 1-17 Inference of R0 and Transmission Heterogeneity from the Size Distribution of Stuttering Chains
by Seth Blumberg & James O Lloyd-Smith - 1-17 Sparse Coding Can Predict Primary Visual Cortex Receptive Field Changes Induced by Abnormal Visual Input
by Jonathan J Hunt & Peter Dayan & Geoffrey J Goodhill
April 2013, Volume 9, Issue 4
- 1-6 A Healthy Fear of the Unknown: Perspectives on the Interpretation of Parameter Fits from Computational Models in Neuroscience
by Matthew R Nassar & Joshua I Gold - 1-9 A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase
by Lin-Tai Da & Fátima Pardo Avila & Dong Wang & Xuhui Huang - 1-10 Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations
by Daniel L Parton & Alex Tek & Marc Baaden & Mark S P Sansom - 1-10 Biomarker Discovery by Sparse Canonical Correlation Analysis of Complex Clinical Phenotypes of Tuberculosis and Malaria
by Juho Rousu & Daniel D Agranoff & Olugbemiro Sodeinde & John Shawe-Taylor & Delmiro Fernandez-Reyes - 1-12 Steered Molecular Dynamics Simulations of a Type IV Pilus Probe Initial Stages of a Force-Induced Conformational Transition
by Joseph L Baker & Nicolas Biais & Florence Tama - 1-12 Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps
by Andrei Zinovyev & Inna Kuperstein & Emmanuel Barillot & Wolf-Dietrich Heyer - 1-13 Ab Initio Modeling and Experimental Assessment of Janus Kinase 2 (JAK2) Kinase-Pseudokinase Complex Structure
by Xiaobo Wan & Yue Ma & Christopher L McClendon & Lily Jun-shen Huang & Niu Huang - 1-14 Localization of Protein Aggregation in Escherichia coli Is Governed by Diffusion and Nucleoid Macromolecular Crowding Effect
by Anne-Sophie Coquel & Jean-Pascal Jacob & Mael Primet & Alice Demarez & Mariella Dimiccoli & Thomas Julou & Lionel Moisan & Ariel B Lindner & Hugues Berry - 1-14 Human Germline Antibody Gene Segments Encode Polyspecific Antibodies
by Jordan R Willis & Bryan S Briney & Samuel L DeLuca & James E Crowe Jr & Jens Meiler - 1-15 Data-Driven Modeling of Src Control on the Mitochondrial Pathway of Apoptosis: Implication for Anticancer Therapy Optimization
by Annabelle Ballesta & Jonathan Lopez & Nikolay Popgeorgiev & Philippe Gonzalo & Marie Doumic & Germain Gillet - 1-15 Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation
by Gabriela V Cohen Freue & Anna Meredith & Derek Smith & Axel Bergman & Mayu Sasaki & Karen K Y Lam & Zsuzsanna Hollander & Nina Opushneva & Mandeep Takhar & David Lin & Janet Wilson-McManus & Robert Balshaw & Paul A Keown & Christoph H Borchers & Bruce McManus & Raymond T Ng & W Robert McMaster & for the Biomarkers in Transplantation and the NCE CECR Prevention of Organ Failure Centre of Excellence Teams - 1-15 Lifespan Differences in Hematopoietic Stem Cells are Due to Imperfect Repair and Unstable Mean-Reversion
by Hans B Sieburg & Giulio Cattarossi & Christa E Muller-Sieburg - 1-15 Noise Suppression and Surplus Synchrony by Coincidence Detection
by Matthias Schultze-Kraft & Markus Diesmann & Sonja Grün & Moritz Helias - 1-17 Learning Multisensory Integration and Coordinate Transformation via Density Estimation
by Joseph G Makin & Matthew R Fellows & Philip N Sabes - 1-21 Optimal Balance of the Striatal Medium Spiny Neuron Network
by Adam Ponzi & Jeffery R Wickens - 1-30 Bayesian Computation Emerges in Generic Cortical Microcircuits through Spike-Timing-Dependent Plasticity
by Bernhard Nessler & Michael Pfeiffer & Lars Buesing & Wolfgang Maass
March 2013, Volume 9, Issue 3
- 1-8 Chaste: An Open Source C++ Library for Computational Physiology and Biology
by Gary R Mirams & Christopher J Arthurs & Miguel O Bernabeu & Rafel Bordas & Jonathan Cooper & Alberto Corrias & Yohan Davit & Sara-Jane Dunn & Alexander G Fletcher & Daniel G Harvey & Megan E Marsh & James M Osborne & Pras Pathmanathan & Joe Pitt-Francis & James Southern & Nejib Zemzemi & David J Gavaghan - 1-9 Bursts of Vertex Activation and Epidemics in Evolving Networks
by Luis E C Rocha & Vincent D Blondel - 1-9 Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network
by Jialiang Huang & Chaoqun Niu & Christopher D Green & Lun Yang & Hongkang Mei & Jing-Dong J Han - 1-9 The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks
by Clive G Bowsher & Margaritis Voliotis & Peter S Swain - 1-9 Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models
by Per Larsson & Peter M Kasson - 1-9 Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
by Silvio a Beccara & Tatjana Škrbić & Roberto Covino & Cristian Micheletti & Pietro Faccioli - 1-9 Policy Resistance Undermines Superspreader Vaccination Strategies for Influenza
by Chad R Wells & Eili Y Klein & Chris T Bauch - 1-10 Stability and Responsiveness in a Self-Organized Living Architecture
by Simon Garnier & Tucker Murphy & Matthew Lutz & Edward Hurme & Simon Leblanc & Iain D Couzin - 1-10 Druggable Protein Interaction Sites Are More Predisposed to Surface Pocket Formation than the Rest of the Protein Surface
by David K Johnson & John Karanicolas - 1-11 Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences
by Dazhi Jiao & Yuzhen Ye & Haixu Tang - 1-11 Bayesian Estimation of Mixture Models with Prespecified Elements to Compare Drug Resistance in Treatment-Naïve and Experienced Tuberculosis Cases
by Alane Izu & Ted Cohen & Victor DeGruttola - 1-12 Explaining the Determinants of First Phase HIV Decay Dynamics through the Effects of Stage-dependent Drug Action
by James B Gilmore & Anthony D Kelleher & David A Cooper & John M Murray - 1-12 Split Histidine Kinases Enable Ultrasensitivity and Bistability in Two-Component Signaling Networks
by Munia Amin & Steven L Porter & Orkun S Soyer - 1-12 A Model of Binocular Rivalry and Cross-orientation Suppression
by Christopher P Said & David J Heeger - 1-12 Collective Cell Motion in an Epithelial Sheet Can Be Quantitatively Described by a Stochastic Interacting Particle Model
by Néstor Sepúlveda & Laurence Petitjean & Olivier Cochet & Erwan Grasland-Mongrain & Pascal Silberzan & Vincent Hakim - 1-12 Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model
by Libin Rong & Jeremie Guedj & Harel Dahari & Daniel J Coffield Jr & Micha Levi & Patrick Smith & Alan S Perelson - 1-13 Processing of Multi-dimensional Sensorimotor Information in the Spinal and Cerebellar Neuronal Circuitry: A New Hypothesis
by Anton Spanne & Henrik Jörntell - 1-13 Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage
by Katarzyna Bozek & Thomas Lengauer & Saleta Sierra & Rolf Kaiser & Francisco S Domingues - 1-13 Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection
by Richard P Mann & Andrea Perna & Daniel Strömbom & Roman Garnett & James E Herbert-Read & David J T Sumpter & Ashley J W Ward - 1-13 An Integrated Computational/Experimental Model of Lymphoma Growth
by Hermann B Frieboes & Bryan R Smith & Yao-Li Chuang & Ken Ito & Allison M Roettgers & Sanjiv S Gambhir & Vittorio Cristini - 1-14 Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes
by Christopher Y Park & Aaron K Wong & Casey S Greene & Jessica Rowland & Yuanfang Guan & Lars A Bongo & Rebecca D Burdine & Olga G Troyanskaya - 1-14 Noise-invariant Neurons in the Avian Auditory Cortex: Hearing the Song in Noise
by R Channing Moore & Tyler Lee & Frédéric E Theunissen - 1-14 RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State
by Nisha Rajagopal & Wei Xie & Yan Li & Uli Wagner & Wei Wang & John Stamatoyannopoulos & Jason Ernst & Manolis Kellis & Bing Ren - 1-14 Automated Analysis of a Diverse Synapse Population
by Brad Busse & Stephen Smith - 1-14 Stimulus-dependent Maximum Entropy Models of Neural Population Codes
by Einat Granot-Atedgi & Gašper Tkačik & Ronen Segev & Elad Schneidman - 1-15 Optimal Vaccine Allocation for the Early Mitigation of Pandemic Influenza
by Laura Matrajt & M Elizabeth Halloran & Ira M Longini Jr - 1-15 Embedding Responses in Spontaneous Neural Activity Shaped through Sequential Learning
by Tomoki Kurikawa & Kunihiko Kaneko - 1-16 A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana
by Christoph Schmal & Peter Reimann & Dorothee Staiger - 1-16 Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment
by Wei Zhang & Takayo Ota & Viji Shridhar & Jeremy Chien & Baolin Wu & Rui Kuang - 1-16 The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum
by Rasmus Agren & Liming Liu & Saeed Shoaie & Wanwipa Vongsangnak & Intawat Nookaew & Jens Nielsen - 1-16 Signaling Pathways Involved in Striatal Synaptic Plasticity are Sensitive to Temporal Pattern and Exhibit Spatial Specificity
by BoHung Kim & Sarah L Hawes & Fawad Gillani & Lane J Wallace & Kim T Blackwell - 1-17 Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology
by Tina Toni & Bruce Tidor - 1-17 Differential Expression Analysis for Pathways
by Winston A Haynes & Roger Higdon & Larissa Stanberry & Dwayne Collins & Eugene Kolker - 1-18 Sustained Firing of Model Central Auditory Neurons Yields a Discriminative Spectro-temporal Representation for Natural Sounds
by Michael A Carlin & Mounya Elhilali - 1-21 Modelling the Emergence and Dynamics of Perceptual Organisation in Auditory Streaming
by Robert W Mill & Tamás M Bőhm & Alexandra Bendixen & István Winkler & Susan L Denham
February 2013, Volume 9, Issue 2
- 1-2 Let's Make Those Book Chapters Open Too!
by Philip E Bourne - 1-6 Optimal Properties of Analog Perceptrons with Excitatory Weights
by Claudia Clopath & Nicolas Brunel - 1-9 An Entropic Mechanism of Generating Selective Ion Binding in Macromolecules
by Michael Thomas & Dylan Jayatilaka & Ben Corry - 1-9 No Evidence for an Item Limit in Change Detection
by Shaiyan Keshvari & Ronald van den Berg & Wei Ji Ma - 1-9 Spartan: A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems
by Kieran Alden & Mark Read & Jon Timmis & Paul S Andrews & Henrique Veiga-Fernandes & Mark Coles - 1-10 Standard Anatomical and Visual Space for the Mouse Retina: Computational Reconstruction and Transformation of Flattened Retinae with the Retistruct Package
by David C Sterratt & Daniel Lyngholm & David J Willshaw & Ian D Thompson - 1-11 Virus Neutralisation: New Insights from Kinetic Neutralisation Curves
by Carsten Magnus - 1-11 Cost and Effects of Different Admission Screening Strategies to Control the Spread of Methicillin-resistant Staphylococcus aureus
by Tanya Gurieva & Martin C J Bootsma & Marc J M Bonten - 1-11 Collective States, Multistability and Transitional Behavior in Schooling Fish
by Kolbjørn Tunstrøm & Yael Katz & Christos C Ioannou & Cristián Huepe & Matthew J Lutz & Iain D Couzin - 1-13 Evidence for Model-based Computations in the Human Amygdala during Pavlovian Conditioning
by Charlotte Prévost & Daniel McNamee & Ryan K Jessup & Peter Bossaerts & John P O'Doherty - 1-13 Multi-Population Classical HLA Type Imputation
by Alexander Dilthey & Stephen Leslie & Loukas Moutsianas & Judong Shen & Charles Cox & Matthew R Nelson & Gil McVean